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<head><title>Quick_Start</title>
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<body
        class="c6"><p class="c0"><span class="c4">Quick Start for Multi-Scale Association
Explorer </span></p>

<p class="c1 c0"><span class="c4"></span></p>

<p
        class="c0"><span>The Multi-Scale Association Explorer (MSAE) enables the exploration of associations derived from
genomic, clinical, and other biomedical data features. &nbsp;</span></p>

<p
        class="c1 c0"><span></span></p>

<p class="c0"><span>The MSAE
 can be used in many ways. &nbsp;Four use cases are: </span></p>

<p
        class="c0"><span>&nbsp;</span></p>
<ol class="c3" start="1">
    <li class="c2
c0"><span>Examine a specific gene</span></li>
    <li class="c0 c2"><span>Examine a
particular data type such as Gene Expression or DNA Methylation</span></li>
    <li
            class="c2 c0"><span>Examine a chromosomal region</span></li>
    <li class="c2
c0"><span>Examine association values with a particular value or range of
values. &nbsp;</span></li>
</ol>
<p class="c1 c0"><span></span></p>

The following examples begin from the dataset located at: <a target="_blank" href="http://explorer.cancerregulome.org/re/?dataset=gbm_1006_nomask">
        http://explorer.cancerregulome.org/re/?dataset=gbm_1006_nomask</a>
<p
        class="c0"><span>Below is an example of examining a specific gene in the MSAE:</span></p>

<p class="c1 c0"><span></span></p>

<p
        class="c1 c0"><span></span></p>

<p class="c0"><span>1. Gene Search for Gene
Expression - RPS4Y1</span></p>

<p class="c0"><span>In the filter window, select
Gene Expression under Type. &nbsp;Then type RPS4Y1 in the Label Box. &nbsp;Click
on Filter.</span></p>

<p class="c1 c0"><span></span></p>

<p class="c0"><img src="images/msae_gene_filterpanel.png"></p>

<p class="c1
c0"><span></span></p>

<p class="c0"><span>2. Use your mouse to place the arrow
over the blue tick representing RPS4Y1 gene expression to see the information
card.</span></p>

<p class="c1 c0"><span></span></p>

<p class="c0"><span>3. Pin the
information card to the window. &nbsp;To do this, click on the &ldquo;T&rdquo;
    in the upper left corner. &nbsp;The T will switch over to an &ldquo;O&rdquo;
    after pinning. <a target="_blank" href="/help/msae/video/tooltips.html">Information Card Video Tutorial</a>
</span></p>

<p class="c1 c0"><span></span></p>

<p class="c0"><img src="images/msae_gene_infocard.png">
</p>

<p class="c1
c0"><span></span></p>

<p class="c0"><span>4. To see additional information about
this gene, click on one of the links at the bottom of the information
card.</span></p>

<p class="c1 c0"><span></span></p>

<p class="c0"><span>5. Click
on the blue tick to open the RPS4Y1 feature in the chromosome-level
view.</span></p>

<p class="c1 c0"><span></span></p>

<p class="c0"><span>6. In the
chromosome-level view, you can see the RPS4Y1 feature on the feature types and
assocation panels.<a target="_blank" href="/help/msae/video/linear_browser.html">Linear Browser Video
        Tutorial</a>
</span><br><br><img src="images/msae_linear_gene.png">
    </span></p>

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c0"><span></span></p>

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c0"><span></span></p>

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c0"><span></span></p>

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